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| Status |
Public on Jan 25, 2021 |
| Title |
Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [ChIP-Seq] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
TATA box-containing promoters are often associated with tissue-specific effector genes, genes that are important for the structure and function of differentiated tissues. The underlying reason for this promoter preference is unclear, in part because tissue-specific genes have not been studied as widely as genes that drive embryonic development. To fill this gap in knowledge, we performed single-cell RNA-seq on differentiated cells derived from the late Drosophila embryo, identified the various tissues and analyzed the relationship between promoter types and gene expression across tissues. Our analysis confirmed the usage of TATA-containing promoters but revealed that tissue-specific effector genes are induced by two distinct promoter types, which have different mechanisms of regulation by RNA polymerase II (Pol II) and different expression characteristics. TATA-enriched promoters are highly tissue-specific and are only occupied by Pol II in the tissue in which they are active; the other promoter type is depleted in TATA motifs and shows high levels of paused Pol II throughout the embryo, even in tissues where the genes are not expressed. Interestingly, the single-cell RNA-seq data revealed that the paused promoters have more robust expression when expressed, but have higher background expression in tissues where these genes are not expressed. TATA genes, on the other hand, have little background expression, but larger variations in expression among the cells that show expression. To explain this difference, we propose that TATA-containing promoters have a higher activation barrier, but preferentially evolve in tissue-specific genes due to their strong activation potential and higher evolvability.
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| Overall design |
ScRNAseq, RNAseq and Tissue Specific ChIP-Seq or ATAC-Seq was performed in Drosphila embryos.
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| Contributor(s) |
Ramalingam V, Natarajan M, Johnston J, Zeitlinger J |
| Citation(s) |
33543829 |
| |
| Submission date |
Sep 18, 2018 |
| Last update date |
Feb 16, 2021 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
jbz@stowers.org
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| Organization name |
Stowers Institute
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platforms (2) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (11)
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| GSM3394953 |
Pol II ChIP in 14-17hrs OregonR embryos Rep1 |
| GSM3394954 |
Pol II ChIP in 14-17hrs OregonR embryos Rep2 |
| GSM3394955 |
Pol II ChIP in 2-4hrs OregonR embryos Rep1 |
| GSM3394956 |
Pol II ChIP in 2-4hrs OregonR embryos Rep2 |
| GSM3394957 |
TFIIB ChIP in 14-17hrs OregonR embryos Rep1 |
| GSM3394958 |
TFIIB ChIP in 14-17hrs OregonR embryos Rep2 |
| GSM3394959 |
TFIIF ChIP in 14-17hrs OregonR embryos Rep1 |
| GSM3394960 |
WCE in 14-17hrs OregonR embryos Rep1 |
| GSM3394961 |
WCE in 14-17hrs OregonR embryos Rep2 |
| GSM3394962 |
WCE in 2-4hrs OregonR embryos Rep1 |
| GSM3394963 |
WCE in 2-4hrs OregonR embryos Rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE120157 |
Two promoter types induce tissue-specific effector genes in the late Drosophila embryo |
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| Relations |
| BioProject |
PRJNA491739 |
| SRA |
SRP162063 |
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